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Phylogenetic applications of the minimum contradiction approach on continuous characters.

Thuillard M, Fraix-Burnet D - Evol. Bioinform. Online (2009)

Bottom Line: We explain how to discover the main structuring characters in a tree.The second set consists of a sample of 100 galaxies.In that second example one shows how to discretize the continuous variables describing physical properties of the galaxies without disrupting the underlying tree structure.

View Article: PubMed Central - PubMed

Affiliation: La Colline, 2072 St-Blaise (Switzerland). thuillweb@hotmail.com

ABSTRACT
We describe the conditions under which a set of continuous variables or characters can be described as an X-tree or a split network. A distance matrix corresponds exactly to a split network or a valued X-tree if, after ordering of the taxa, the variables values can be embedded into a function with at most a local maximum and a local minimum, and crossing any horizontal line at most twice. In real applications, the order of the taxa best satisfying the above conditions can be obtained using the Minimum Contradiction method. This approach is applied to 2 sets of continuous characters. The first set corresponds to craniofacial landmarks in Hominids. The contradiction matrix is used to identify possible tree structures and some alternatives when they exist. We explain how to discover the main structuring characters in a tree. The second set consists of a sample of 100 galaxies. In that second example one shows how to discretize the continuous variables describing physical properties of the galaxies without disrupting the underlying tree structure.

No MeSH data available.


Minimum contradiction matrix Yi,jn on a set of 20 hominid taxa using Pan troglodytes as reference taxon n.
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f10-ebo-2009-033: Minimum contradiction matrix Yi,jn on a set of 20 hominid taxa using Pan troglodytes as reference taxon n.

Mentions: The level of contradiction can be used as an objective criterion to choose the reference node. As discussed in details in Thuillard,11,12 the reference node is an important choice in the presence of contradictions. In our example, the normalized level of contradiction is about 30% lower with Pan troglodytes as reference taxon. This suggests that Pan troglodytes is a better choice than Gorilla gorilla as a reference taxon. Figure 10 shows quite interestingly that the ambiguity concerning H. habilis is removed with Pan troglodytes as reference taxon. H. habilis belongs clearly to Homo. In summary, with the data analyzed here, H. habilis shares some characters with non Homo, but has a majority of characters shared with other Homo specimen, predominantly H. erectus/H. ergaster.


Phylogenetic applications of the minimum contradiction approach on continuous characters.

Thuillard M, Fraix-Burnet D - Evol. Bioinform. Online (2009)

Minimum contradiction matrix Yi,jn on a set of 20 hominid taxa using Pan troglodytes as reference taxon n.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC2747132&req=5

f10-ebo-2009-033: Minimum contradiction matrix Yi,jn on a set of 20 hominid taxa using Pan troglodytes as reference taxon n.
Mentions: The level of contradiction can be used as an objective criterion to choose the reference node. As discussed in details in Thuillard,11,12 the reference node is an important choice in the presence of contradictions. In our example, the normalized level of contradiction is about 30% lower with Pan troglodytes as reference taxon. This suggests that Pan troglodytes is a better choice than Gorilla gorilla as a reference taxon. Figure 10 shows quite interestingly that the ambiguity concerning H. habilis is removed with Pan troglodytes as reference taxon. H. habilis belongs clearly to Homo. In summary, with the data analyzed here, H. habilis shares some characters with non Homo, but has a majority of characters shared with other Homo specimen, predominantly H. erectus/H. ergaster.

Bottom Line: We explain how to discover the main structuring characters in a tree.The second set consists of a sample of 100 galaxies.In that second example one shows how to discretize the continuous variables describing physical properties of the galaxies without disrupting the underlying tree structure.

View Article: PubMed Central - PubMed

Affiliation: La Colline, 2072 St-Blaise (Switzerland). thuillweb@hotmail.com

ABSTRACT
We describe the conditions under which a set of continuous variables or characters can be described as an X-tree or a split network. A distance matrix corresponds exactly to a split network or a valued X-tree if, after ordering of the taxa, the variables values can be embedded into a function with at most a local maximum and a local minimum, and crossing any horizontal line at most twice. In real applications, the order of the taxa best satisfying the above conditions can be obtained using the Minimum Contradiction method. This approach is applied to 2 sets of continuous characters. The first set corresponds to craniofacial landmarks in Hominids. The contradiction matrix is used to identify possible tree structures and some alternatives when they exist. We explain how to discover the main structuring characters in a tree. The second set consists of a sample of 100 galaxies. In that second example one shows how to discretize the continuous variables describing physical properties of the galaxies without disrupting the underlying tree structure.

No MeSH data available.